Distribution and Quantification of Antibiotic Resistant Genes and Bacteria across Agricultural and Non-Agricultural Metagenomes

Durso, Lisa M.; Miller, Daniel N.; Wienhold, Brian J.

doi:10.1371/journal.pone.0048325

Cited by 116 publications

(98 citation statements)

References 30 publications

(25 reference statements)

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“…In this study, we characterized the microbiomes and resistomes of different sectors (fecal, manure, and soil) of five dairy farms, using a metagenomics approach. Our findings indicate that the proportion of AR genes (resistome) accounted to <1.0% of the total gene content similar to the abundance of resistomes reported from the cow rumen (0.97%; Durso et al, 2012) and manure (three AR genes/GB of data; Wichmann et al, 2014).…”

Section: Discussionsupporting

confidence: 82%

“…Taxonomic characterization revealed the abundance of Bacteroidetes and Firmicutes in fecal and manure microbiomes similar to the findings of Durso et al (2012), except for farm 9, which had a higher abundance of Proteobacteria in Farm Number 2 5 6 9 12 2 5 6 9 12 2 6 9 12 2 5 6 9 12 the fecal samples. Our results for microbial profiles in soil samples are similar to Forsberg et al (2012) and Walsh and Duffy (2013), who reported the prevalence of Proteobacteria in soil samples.…”

Section: Discussionsupporting

confidence: 68%

“…Recent evidences (Durso et al, 2011(Durso et al, , 2012Wichmann et al, 2014) clearly demonstrate that manure from farm animals represents a huge reservoir for AR genes. These reports indicate that phylogenetically unrelated bacterial species present in manure samples contained similar multidrug AR genes.…”

Section: Introductionmentioning

confidence: 99%

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Metagenomic Evidence of the Prevalence and Distribution Patterns of Antimicrobial Resistance Genes in Dairy Agroecosystems

Pitta

Dou

Kumar

et al. 2016

Foodborne Pathogens and Disease

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Antimicrobial resistance (AR) is a global problem with serious implications for public health. AR genes are frequently detected on animal farms, but little is known about their origin and distribution patterns. We hypothesized that AR genes can transfer from animal feces to the environment through manure, and to this end, we characterized and compared the resistomes (collections of AR genes) of animal feces, manure, and soil samples collected from five dairy farms using a metagenomics approach. Resistomes constituted only up to 1% of the total gene content, but were variable by sector and also farm. Broadly, the identified AR genes were associated with 18 antibiotic resistances classes across all samples; however, the most abundant genes were classified under multidrug transporters (44.75%), followed by resistance to vancomycin (12.48%), tetracycline (10.52%), bacitracin (10.43%), beta-lactam resistance (7.12%), and MLS efflux pump (6.86%) antimicrobials. The AR gene profiles were variable between farms. Farm 09 was categorized as a high risk farm, as a greater proportion of AR genes were common to at least three sectors, suggesting possible horizontal transfer of AR genes. Taxonomic characterization of AR genes revealed that a majority of AR genes were associated with the phylum Proteobacteria. Nonetheless, there were several members of Bacteroidetes, particularly Bacteroides genus and several lineages from Firmicutes that carried similar AR genes in different sectors, suggesting a strong potential for horizontal transfer of AR genes between unrelated bacterial hosts in different sectors of the farms. Further studies are required to affirm the horizontal gene transfer mechanisms between microbiomes of different sectors in animal agroecosystems.

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Section: Discussionsupporting

confidence: 82%

Section: Discussionsupporting

confidence: 68%

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Metagenomic Evidence of the Prevalence and Distribution Patterns of Antimicrobial Resistance Genes in Dairy Agroecosystems

Pitta

Dou

Kumar

et al. 2016

Foodborne Pathogens and Disease

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“…Surprisingly, however, many other studies have shown that the widespread occurrence of antibiotic resistance genes are sometimes unrelated to human activities. For example, antibiotic resistance genes have been documented in pristine habitats such as Alaskan soil, Antarctic marine waters, ancient sediment samples, glacier ice cores, and nonagricultural soil (2,(10)(11)(12)(13)(14)(15), often in abundances well above trace levels. These findings raise questions about the stable maintenance of antibiotic resistance genes in the absence of human-mediated selective pressures.…”

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confidence: 99%

Recovery of Plasmid pEMB1, Whose Toxin-Antitoxin System Stabilizes an Ampicillin Resistance-Conferring β-Lactamase Gene in Escherichia coli, from Natural Environments

Lee¹,

Jin²,

Park³

et al. 2015

Appl Environ Microbiol

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c Non-culture-based procedures were used to investigate plasmids showing ampicillin resistance properties in two different environments: remote mountain soil (Mt. Jeombong) and sludge (Tancheon wastewater treatment plant). Total DNA extracted from the environmental samples was directly transformed into Escherichia coli TOP10, and a single and three different plasmids were obtained from the mountain soil and sludge samples, respectively. Interestingly, the restriction fragment length polymorphism pattern of the plasmid from the mountain soil sample, designated pEMB1, was identical to the pattern of one of the three plasmids from the sludge sample. Complete DNA sequencing of plasmid pEMB1 (8,744 bp) showed the presence of six open reading frames, including a ␤-lactamase gene. Using BLASTX, the orf5 and orf6 genes were suggested to encode a CopG family transcriptional regulator and a plasmid stabilization system, respectively. Functional characterization of these genes using a knockout orf5 plasmid (pEMB1⌬parD) and the cloning and expression of orf6 (pET21bparE) indicated that these genes were antitoxin (parD) and toxin (parE) genes. Plasmid stability tests using pEMB1 and pEMB1⌬parDE in E. coli revealed that the orf5 and orf6 genes enhanced plasmid maintenance in the absence of ampicillin. Using a PCR-based survey, pEMB1-like plasmids were additionally detected in samples from other human-impacted sites (sludge samples) and two other remote mountain soil samples, suggesting that plasmids harboring a ␤-lactamase gene with a ParD-ParE toxin-antitoxin system occurs broadly in the environment. This study extends knowledge about the dissemination and persistence of antibiotic resistance genes in naturally occurring microbial populations.A ntibiotic treatments have been one of the most effective ways to control infectious diseases, but the frequency of detecting bacteria that are resistant to antibiotics from environmental samples has recently increased (1). It is generally thought that the use of antibiotics as human and veterinary medicine or as animal feed additives is a major driving force in the development of antibioticresistant bacteria and the dissemination of antibiotic resistance genes (2-4). Indeed, high levels of antibiotic resistance genes have been identified in a variety of human-impacted milieus such as wastewater sludge, soils fertilized with manure, and river waters that have been frequently exposed to antibiotics (5-9). Surprisingly, however, many other studies have shown that the widespread occurrence of antibiotic resistance genes are sometimes unrelated to human activities. For example, antibiotic resistance genes have been documented in pristine habitats such as Alaskan soil, Antarctic marine waters, ancient sediment samples, glacier ice cores, and nonagricultural soil (2, 10-15), often in abundances well above trace levels. These findings raise questions about the stable maintenance of antibiotic resistance genes in the absence of human-mediated selective pressures. It should also be noted that s...

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“…They are excreted as parent compound conjugates, or as oxidation, hydroxylation, dealkylation, and decarboxylation products of the parent compound (26). Acute toxicity of FQs generally is low; however, their residues in food may pose a hazard to consumers through emergence of drugresistant bacteria (5,9,21). The adverse effects associated with FQs include gastrointestinal effects (nausea, vomiting, diarrhoea), dermatologic effects (phototoxicity), tendinopathy, and CNS reactions (2).…”

Section: Introductionmentioning

confidence: 99%

Influence of fluoroquinolones on viability of Balb/c 3T3 and HepG2 cells

Radko

Minta

Stypuła-Trębas

2013

Bulletin of the Veterinary Institute in Pulawy

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The cytotoxic potential of fluoroquinolones (enrofloxacin, ciprofloxacin, difloxacin, sarafloxacin, danofloxacin, norfloxacin and marbofloxacin) was investigated using mouse fibroblasts Balb/c 3T3 and human hepatoma HepG2 cell lines. The cells were exposed for 24, 48, and 72 h to drugs at eight concentrations ranged from 0.78 to 100 µg/mL. Four independent cytotoxicity assays were applied, in which various endpoints were assessed: mitochondrial activity -MTT reduction, lysosomal activity -neutral red uptake, total protein content, and cellular membrane integrity -lactate dehydrogenase release. Mean effective cytotoxic concentrations (EC 50 ) calculated at different time points from concentration-response curves ranged from 10 to 100 µg/mL. The most affected endpoint in both cell lines was mitochondrial activity. The EC 50-MTT-72 h <10 µg/mL was found for difloxacin, marbofloxacin (fibroblasts), sarafloxacin, and norfloxacin (HepG2). The data shows that cytotoxicity of the fluoroquinolones appears after longer exposure of both cell cultures to these compounds.

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Distribution and Quantification of Antibiotic Resistant Genes and Bacteria across Agricultural and Non-Agricultural Metagenomes

Cited by 116 publications

References 30 publications

Metagenomic Evidence of the Prevalence and Distribution Patterns of Antimicrobial Resistance Genes in Dairy Agroecosystems

Metagenomic Evidence of the Prevalence and Distribution Patterns of Antimicrobial Resistance Genes in Dairy Agroecosystems

Recovery of Plasmid pEMB1, Whose Toxin-Antitoxin System Stabilizes an Ampicillin Resistance-Conferring β-Lactamase Gene in Escherichia coli, from Natural Environments

Influence of fluoroquinolones on viability of Balb/c 3T3 and HepG2 cells

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